Due to their good color rendering ability, white light-emitting diodes (WLEDs) with conventional phosphor and quantum dots (QDs) are gaining increasing attention. However, their optical and thermal performances are still limited especially for the ones with QDs-phosphor mixed nanocomposites. In this work, we propose a novel packaging scheme with horizontally layered QDs-phosphor nanocomposites to obtain an enhanced optical and thermal performance for WLEDs. Three different WLEDs, including QDs-phosphor mixed type, QDs-outside type, and QDs-inside type, were fabricated and compared. With 30 wt. % phosphor and 0.15 wt. % QDs nanocomposite, the QDs-outside type WLED shows a 21.8% increase of luminous efficiency, better color rendering ability, and a 27.0% decrease of the maximum nanocomposite temperature at 400 mA, compared with the mixed-type WLED. The reduced re-absorption between phosphor and QDs is responsible for the performance enhancement when they are separated. However, such reduced absorption can be traded off by the improper layered configuration, which is demonstrated by the worst performance of the QDs-inside type. Further, we demonstrate that the higher energy transfer efficiency between excitation light and nanocomposite in the QDs-outside type WLED is the key reason for its enhanced optical and thermal performance.